Harvest for US Minor Outlying Islands Species List Created 17 Oct 11:07

Stage: completed
Fetched: 17 Oct 11:07
Validated: 17 Oct 11:07
Deltas Created 17 Oct 11:07
Units Normalized: 17 Oct 11:07
Ancestry Built: 17 Oct 11:07
Nodes Matched: 17 Oct 11:07
Names Parsed: 17 Oct 11:07
New Models Stored: 17 Oct 11:07
Indexed: 17 Oct 11:07
Completed: 17 Oct 11:09
Time to Harvest: less than a minute

Harvesting Log

(139 lines)
# Logfile created on 2019-10-17 11:07:42 -0400 by logger.rb/56815
[START] [2019-10-17 11:07:42] logged process
[START] [2019-10-17 11:07:42] create_harvest_instance
[STOP] [2019-10-17 11:07:42] create_harvest_instance
[START] [2019-10-17 11:07:42] fetch_files
[STOP] [2019-10-17 11:07:42] fetch_files
[START] [2019-10-17 11:07:42] validate_each_file
[STOP] [2019-10-17 11:07:42] validate_each_file
[START] [2019-10-17 11:07:42] convert_to_csv
[CMD] [2019-10-17 11:07:42] /usr/bin/sort /app/public/converted_csv/us_minor_outlyin_refs_17705.csv > /app/public/converted_csv/us_minor_outlyin_refs_17705.csv_sorted
[CMD] [2019-10-17 11:07:42] /usr/bin/sort /app/public/converted_csv/us_minor_outlyin_nodes_17706.csv > /app/public/converted_csv/us_minor_outlyin_nodes_17706.csv_sorted
[CMD] [2019-10-17 11:07:42] /usr/bin/sort /app/public/converted_csv/us_minor_outlyin_occurrences_17707.csv > /app/public/converted_csv/us_minor_outlyin_occurrences_17707.csv_sorted
[CMD] [2019-10-17 11:07:42] /usr/bin/sort /app/public/converted_csv/us_minor_outlyin_measurements_17708.csv > /app/public/converted_csv/us_minor_outlyin_measurements_17708.csv_sorted
[STOP] [2019-10-17 11:07:43] convert_to_csv
[START] [2019-10-17 11:07:43] calculate_delta
[CMD] [2019-10-17 11:07:43] echo "0a" > /app/public/diff/us_minor_outlyin_refs_17705.diff
[CMD] [2019-10-17 11:07:43] tail -n +1 /app/public/converted_csv/us_minor_outlyin_refs_17705.csv >> /app/public/diff/us_minor_outlyin_refs_17705.diff
[CMD] [2019-10-17 11:07:43] echo "." >> /app/public/diff/us_minor_outlyin_refs_17705.diff
[CMD] [2019-10-17 11:07:43] echo "0a" > /app/public/diff/us_minor_outlyin_nodes_17706.diff
[CMD] [2019-10-17 11:07:43] tail -n +1 /app/public/converted_csv/us_minor_outlyin_nodes_17706.csv >> /app/public/diff/us_minor_outlyin_nodes_17706.diff
[CMD] [2019-10-17 11:07:43] echo "." >> /app/public/diff/us_minor_outlyin_nodes_17706.diff
[CMD] [2019-10-17 11:07:43] echo "0a" > /app/public/diff/us_minor_outlyin_occurrences_17707.diff
[CMD] [2019-10-17 11:07:43] tail -n +1 /app/public/converted_csv/us_minor_outlyin_occurrences_17707.csv >> /app/public/diff/us_minor_outlyin_occurrences_17707.diff
[CMD] [2019-10-17 11:07:43] echo "." >> /app/public/diff/us_minor_outlyin_occurrences_17707.diff
[CMD] [2019-10-17 11:07:43] echo "0a" > /app/public/diff/us_minor_outlyin_measurements_17708.diff
[CMD] [2019-10-17 11:07:43] tail -n +1 /app/public/converted_csv/us_minor_outlyin_measurements_17708.csv >> /app/public/diff/us_minor_outlyin_measurements_17708.diff
[CMD] [2019-10-17 11:07:44] echo "." >> /app/public/diff/us_minor_outlyin_measurements_17708.diff
[STOP] [2019-10-17 11:07:44] calculate_delta
[START] [2019-10-17 11:07:44] parse_diff_and_store
[INFO] [2019-10-17 11:07:44] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-17 11:07:44] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-17 11:07:44] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-17 11:07:44] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-17 11:07:44] Storing 2 References
[INFO] [2019-10-17 11:07:44] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-17 11:07:44] Average Time: 0.0
[INFO] [2019-10-17 11:07:44] Total Time: 1s
[INFO] [2019-10-17 11:07:44] Storing 48 ScientificNames
[INFO] [2019-10-17 11:07:44] Processing group of 48 in 1 groups of 1000
[INFO] [2019-10-17 11:07:44] Average Time: 0.03
[INFO] [2019-10-17 11:07:44] Total Time: 1s
[INFO] [2019-10-17 11:07:44] Storing 48 Nodes
[INFO] [2019-10-17 11:07:44] Processing group of 48 in 1 groups of 1000
[INFO] [2019-10-17 11:07:44] Average Time: 0.02
[INFO] [2019-10-17 11:07:44] Total Time: 1s
[INFO] [2019-10-17 11:07:44] Storing 18 Occurrences
[INFO] [2019-10-17 11:07:44] Processing group of 18 in 1 groups of 1000
[INFO] [2019-10-17 11:07:44] Average Time: 0.0
[INFO] [2019-10-17 11:07:44] Total Time: 1s
[INFO] [2019-10-17 11:07:44] Storing 36 TraitsReferences
[INFO] [2019-10-17 11:07:44] Processing group of 36 in 1 groups of 1000
[INFO] [2019-10-17 11:07:44] Average Time: 0.01
[INFO] [2019-10-17 11:07:44] Total Time: 1s
[INFO] [2019-10-17 11:07:44] Storing 36 Traits
[INFO] [2019-10-17 11:07:44] Processing group of 36 in 1 groups of 1000
[INFO] [2019-10-17 11:07:44] Average Time: 0.02
[INFO] [2019-10-17 11:07:44] Total Time: 1s
[INFO] [2019-10-17 11:07:44] Storing 36 MetaTraits
[INFO] [2019-10-17 11:07:44] Processing group of 36 in 1 groups of 1000
[INFO] [2019-10-17 11:07:44] Average Time: 0.01
[INFO] [2019-10-17 11:07:44] Total Time: 1s
[STOP] [2019-10-17 11:07:44] parse_diff_and_store
[START] [2019-10-17 11:07:44] resolve_keys
[INFO] [2019-10-17 11:07:48] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-17 11:07:48] traits to occurrences...
[INFO] [2019-10-17 11:07:48] traits to nodes (through occurrences)...
[INFO] [2019-10-17 11:07:48] Traits to sex term...
[INFO] [2019-10-17 11:07:48] Traits to lifestage term...
[INFO] [2019-10-17 11:07:48] MetaTraits to traits...
[INFO] [2019-10-17 11:07:48] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-17 11:07:48] Assocs to occurrences...
[INFO] [2019-10-17 11:07:48] Assocs to nodes...
[INFO] [2019-10-17 11:07:48] Assoc to sex term...
[INFO] [2019-10-17 11:07:48] Assoc to lifestage term...
[STOP] [2019-10-17 11:07:48] resolve_keys
[START] [2019-10-17 11:07:48] hold_for_later_1
[STOP] [2019-10-17 11:07:48] hold_for_later_1
[START] [2019-10-17 11:07:48] hold_for_later_2
[STOP] [2019-10-17 11:07:48] hold_for_later_2
[START] [2019-10-17 11:07:48] resolve_missing_parents
[STOP] [2019-10-17 11:07:48] resolve_missing_parents
[START] [2019-10-17 11:07:48] rebuild_nodes
[START] [2019-10-17 11:07:48] Flattener#flatten
[START] [2019-10-17 11:07:48] Flattener#study_resource
[START] [2019-10-17 11:07:48] Flattener#build_ancestry
[STOP] [2019-10-17 11:07:48] Flattener#build_ancestry
[INFO] [2019-10-17 11:07:48] 48 ancestry keys
[START] [2019-10-17 11:07:48] build_node_ancestors
[INFO] [2019-10-17 11:07:48] old ancestors deleted.
[STOP] [2019-10-17 11:07:48] build_node_ancestors
[START] [2019-10-17 11:07:48] Flattener#propagate_ancestor_ids
[STOP] [2019-10-17 11:07:48] Flattener#propagate_ancestor_ids
[STOP] [2019-10-17 11:07:48] Flattener#flatten
[STOP] [2019-10-17 11:07:48] rebuild_nodes
[START] [2019-10-17 11:07:48] resolve_missing_media_owners
[STOP] [2019-10-17 11:07:48] resolve_missing_media_owners
[START] [2019-10-17 11:07:48] sanitize_media_verbatims
[STOP] [2019-10-17 11:07:48] sanitize_media_verbatims
[START] [2019-10-17 11:07:48] queue_downloads
[STOP] [2019-10-17 11:07:48] queue_downloads
[START] [2019-10-17 11:07:48] parse_names
[WARN] [2019-10-17 11:07:48] I see 48 names which still need to be parsed.
[STOP] [2019-10-17 11:07:49] parse_names
[START] [2019-10-17 11:07:49] denormalize_canonical_names_to_nodes
[STOP] [2019-10-17 11:07:49] denormalize_canonical_names_to_nodes
[START] [2019-10-17 11:07:49] match_nodes
[START] [2019-10-17 11:07:49] map_all_nodes_to_pages
[STOP] [2019-10-17 11:07:53] map_all_nodes_to_pages
[INFO] [2019-10-17 11:07:53] ZERO unmatched nodes (of 48)! Nicely done.
[START] [2019-10-17 11:07:53] update_nodes
[STOP] [2019-10-17 11:07:53] update_nodes
[STOP] [2019-10-17 11:07:53] match_nodes
[START] [2019-10-17 11:07:53] reindex_search
[STOP] [2019-10-17 11:07:53] reindex_search
[START] [2019-10-17 11:07:53] normalize_units
[STOP] [2019-10-17 11:07:53] normalize_units
[START] [2019-10-17 11:07:53] calculate_statistics
[STOP] [2019-10-17 11:07:53] calculate_statistics
[START] [2019-10-17 11:07:53] complete_harvest_instance
[START] [2019-10-17 11:07:53] overall_tsv_creation
[INFO] [2019-10-17 11:07:53] Processing group of 48 in 1 batches of 10000
[INFO] [2019-10-17 11:08:35] 18 Traits (unfiltered)...
[INFO] [2019-10-17 11:08:47] 18 Traits (filtered)...
[INFO] [2019-10-17 11:08:47] 0 Associations (filtered)...
[INFO] [2019-10-17 11:09:23] 90 metadata added.
[INFO] [2019-10-17 11:09:23] 0 metadata added.
[INFO] [2019-10-17 11:09:23] Average Time: 69.33
[INFO] [2019-10-17 11:09:23] Total Time: 1m30s
[STOP] [2019-10-17 11:09:23] overall_tsv_creation
[INFO] [2019-10-17 11:09:23] Done. Check your files:
[INFO] [2019-10-17 11:09:23] (48 lines) /app/public/data/us_minor_outlyin/publish_nodes.tsv
[INFO] [2019-10-17 11:09:23] (225 lines) /app/public/data/us_minor_outlyin/publish_node_ancestors.tsv
[INFO] [2019-10-17 11:09:23] (48 lines) /app/public/data/us_minor_outlyin/publish_scientific_names.tsv
[INFO] [2019-10-17 11:09:23] (19 lines) /app/public/data/us_minor_outlyin/publish_traits.tsv
[INFO] [2019-10-17 11:09:23] (91 lines) /app/public/data/us_minor_outlyin/publish_metadata.tsv
[STOP] [2019-10-17 11:09:23] complete_harvest_instance
[START] [2019-10-17 11:09:23] completed
[STOP] [2019-10-17 11:09:23] completed
[STOP] [2019-10-17 11:09:23] logged process, took 101.89

Latest Process